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CunliangGengCunliangGeng
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Add test file
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‎install-nplinker-deps‎

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#!/bin/bash
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# User should create virutal env to install nplinker and dependencies
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# Do not use pip install --user nplinker
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# Set script to exit immediately if any command fails
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set -e
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#------------------------------------------------------------------------------
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# Creat installation path
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#------------------------------------------------------------------------------
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# Get python install prefix
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if command -v python &> /dev/null; then
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PY_PATH=$(python -c "import sys; print(sys.prefix)")
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elif command -v python3 &> /dev/null; then
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PY_PATH=$(python3 -c "import sys; print(sys.prefix)")
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else
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echo "❌ Error: python NOT FOUND"
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exit
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fi
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# check the path of this script
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if [[ $(command -v install-nplinker-deps) != $PY_PATH/bin/install-nplinker-deps ]]; then
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echo "❌ Error: command `install-nplinker-deps` invoked from bad path;"
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echo "Please install nplinker with `pip install nplinker` and then re-run this command."
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exit
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fi
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# create dependecy install path
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cd $PY_PATH
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[[ -d nplinker_lib ]] || mkdir nplinker_lib
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LIB_PATH=$PY_PATH/nplinker_lib
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cd $LIB_PATH
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echo -e "✅ NPLinker dependecies and databases will be installed in: $LIB_PATH\n"
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#------------------------------------------------------------------------------
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# Check OS system and package manager
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# Not support Windows
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#------------------------------------------------------------------------------
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if [[ "$OSTYPE" == "linux"* ]]; then
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# detect package manager for Linux
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if command -v apt &> /dev/null; then
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echo -e "✅ Package manager is 'apt'\n"
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apt update &> /dev/null
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do_install="apt install -y"
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elif command -v dnf &> /dev/null; then
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echo -e "✅ Package manager is 'dnf'\n"
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do_install="dnf install -y"
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elif command -v yum &> /dev/null; then
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echo -e "✅ Package manager is 'yum'\n"
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do_install="yum install -y"
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else
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echo "Package manager command 'apt' or 'dnf' or 'yum' NOT found."
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exit
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fi
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elif [[ "$OSTYPE" == "darwin"* ]]; then
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# install package manager brew for MacOS if not exist
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! command -v brew &> /dev/null && /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
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do_install="brew install"
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echo -e "✅ Package manager is 'brew'\n"
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else
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echo "Error: NPLinker is not supported on $OSTYPE system, use linux or MacOS system please."
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exit 0
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fi
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install_it(){
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echo -e "🔥 Start installing $1 ..."
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$do_install $1
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echo -e "✅ $1 installed successfully\n"
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}
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#------------------------------------------------------------------------------
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# Install base dependencies if not exist
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#------------------------------------------------------------------------------
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BASE_DEPS="
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git
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wget
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gunzip
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unzip
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"
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for cmd in $BASE_DEPS; do
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if ! command -v $cmd &> /dev/null; then
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install_it $cmd
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fi
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done
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# install gcc compiler (required by FastTree)
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if command -v gcc &> /dev/null; then
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gcc="gcc"
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elif command -v gcc-10 &> /dev/null; then
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gcc="gcc-10"
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elif command -v gcc-11 &> /dev/null; then
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gcc="gcc-11"
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else
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install_it gcc
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gcc="gcc"
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fi
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# upgrade pip and setuptools
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pip install -q -U pip setuptools
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#------------------------------------------------------------------------------
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# Install NPLinker dependencies
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#------------------------------------------------------------------------------
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#--- Install BigScape
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## Note: DO NOT pip install bigscape until its modular version
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echo "🔥 Start installing BigScape ..."
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[[ -d BiG-SCAPE ]] || git clone https://github.com/medema-group/BiG-SCAPE.git
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cd BiG-SCAPE
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git config --add advice.detachedHead false # disable advice
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git config pull.ff only
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git checkout master
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git pull
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git checkout a3ea8c5a4ef0abdb3b6b043a0f2657d3d778ca20 # tag v1.1.4
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pip install -q -U -r requirements.txt
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chmod 754 bigscape.py
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chmod 664 domains_color_file.tsv
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chmod 775 Annotated_MIBiG_reference
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ln -sf $LIB_PATH/BiG-SCAPE/bigscape.py $PY_PATH/bin
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cd ..
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echo -e "✅ BigScape installed successfully\n"
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#--- Install FastTree (not support Windows, required by BigScape)
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# http://www.microbesonline.org/fasttree/
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echo "🔥 Start installing FastTree ..."
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if [[ "$OSTYPE" == "linux"* ]]; then
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$do_install fasttree
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elif [[ "$OSTYPE" == "darwin"* ]]; then
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wget -q --show-progress http://www.microbesonline.org/fasttree/FastTree.c
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$gcc -DNO_SSE -O3 -finline-functions -funroll-loops -Wall -o $PY_PATH/bin/fasttree FastTree.c -lm
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rm FastTree.c
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fi
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echo -e "✅ FastTree installed successfully\n"
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#--- Install Hmmer (not support Windows and ARM64, required by BigScape)
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# brew hmmer not available ARM64 platform (e.g. Apple silicon)
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if ! command -v hmmpress &> /dev/null; then
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install_it hmmer
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fi
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#--- Prepare Pfam database (required by BigScape)
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echo "🔥 Start installing Pfam database ..."
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[[ -e Pfam-A.hmm.gz ]] || wget -q --show-progress ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam34.0/Pfam-A.hmm.gz
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gunzip -f Pfam-A.hmm.gz
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hmmpress -f Pfam-A.hmm
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echo -e "✅ Pfam database installed successfully\n"
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#--- Install canopus_treemap
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echo "🔥 Start installing Canopus"
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pip install -U -q canopus@git+https://github.com/kaibioinfo/canopus_treemap.git
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echo -e "✅ Canopus installed successfully\n"
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#--- Install SIRIUS
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echo "🔥 Start installing Sirius"
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if [[ "$OSTYPE" == "linux"* ]]; then
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wget -q --show-progress https://github.com/boecker-lab/sirius/releases/download/v5.5.5/sirius-5.5.5-linux64-headless.zip
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unzip -q -o sirius-5.5.5-linux64-headless.zip
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ln -sf $LIB_PATH/sirius/bin/sirius $PY_PATH/bin
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rm sirius-5.5.5-linux64-headless.zip
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elif [[ "$OSTYPE" == "darwin"* ]]; then
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wget -q --show-progress https://github.com/boecker-lab/sirius/releases/download/v5.5.5/sirius-5.5.5-osx64-headless.zip
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unzip -q -o sirius-5.5.5-osx64-headless.zip
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ln -sf $LIB_PATH/sirius.app/Contents/MacOS/sirius $PY_PATH/bin
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rm sirius-5.5.5-osx64-headless.zip
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fi
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echo -e "✅ Sirius installed successfully\n"
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echo -e "✅ 🎉 Successfully installed all NPLinker dependencies and databases!\n"

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